nf-core_modules/software/fastqc/test/main.nf

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#!/usr/bin/env nextflow
import java.security.MessageDigest
nextflow.preview.dsl = 2
params.out_dir = "test_output"
params.fastqc_args = ''
params.publish_dir_mode = "copy"
include { FASTQC } from '../main.nf'
private static String getFileChecksum(MessageDigest digest, File file) throws IOException
{
// https://howtodoinjava.com/java/io/how-to-generate-sha-or-md5-file-checksum-hash-in-java/
//Get file input stream for reading the file content
FileInputStream fis = new FileInputStream(file);
//Create byte array to read data in chunks
byte[] byteArray = new byte[1024];
int bytesCount = 0;
//Read file data and update in message digest
while ((bytesCount = fis.read(byteArray)) != -1) {
digest.update(byteArray, 0, bytesCount);
};
//close the stream; We don't need it now.
fis.close();
//Get the hash's bytes
byte[] bytes = digest.digest();
//This bytes[] has bytes in decimal format;
//Convert it to hexadecimal format
StringBuilder sb = new StringBuilder();
for(int i=0; i< bytes.length ;i++)
{
sb.append(Integer.toString((bytes[i] & 0xff) + 0x100, 16).substring(1));
}
//return complete hash
return sb.toString();
}
/**
* Test if FASTQC runs with single-end data
*/
workflow test_single_end {
input_files = Channel.fromPath("data/test_single_end.fastq.gz")
.map {f -> [f.baseName, true, f]}
FASTQC(input_files)
// test that the output looks as expected
FASTQC.out.html.map { name, is_single_end, html_file ->
html_hash = getFileChecksum(MessageDigest.getInstance("MD5"), new File("${html_file}"));
assert name == "test_single_end.fastq"
assert is_single_end == true
assert html_file.getName() == "test_single_end.fastq_fastqc.html"
assert html_hash == "ff04679b50beabdbd9e93db646f5667d"
}
FASTQC.out.zip.map { name, is_single_end, zip_file ->
// NOTE: output zip files do not have a consistent hash
assert name == "test_single_end.fastq"
assert is_single_end == true
assert zip_file.getName() == "test_single_end.fastq_fastqc.zip"
}
}
/**
* Test if FASTQC runs with paired end data
*/
workflow test_paired_end {
input_files = Channel.fromFilePairs("data/test_R{1,2}.fastq.gz")
.map {f -> [f[0], false, f[1]]}
FASTQC(input_files)
// test that the output looks as expected
FASTQC.out.html.map { name, is_single_end, html_files ->
html_r1 = html_files[0]
html_r2 = html_files[1]
html_r1_hash = getFileChecksum(MessageDigest.getInstance("MD5"), new File("${html_r1}"));
html_r2_hash = getFileChecksum(MessageDigest.getInstance("MD5"), new File("${html_r2}"));
assert name == "test_R"
assert is_single_end == false
assert html_r1.getName() == "test_R_1_fastqc.html"
assert html_r2.getName() == "test_R_2_fastqc.html"
assert html_r1_hash == "082c13ce7163ea0f52a66b83cb57b0f0"
assert html_r2_hash == "4ff04ec8da77e3af512f03b8c09a9e04"
}
FASTQC.out.zip.map { name, is_single_end, zip_files ->
zip_r1 = zip_files[0]
zip_r2 = zip_files[1]
// NOTE: output zip files do not have a consistent hash
assert name == "test_R"
assert is_single_end == false
assert zip_r1.getName() == "test_R_1_fastqc.zip"
assert zip_r2.getName() == "test_R_2_fastqc.zip"
}
}
workflow {
test_single_end()
test_paired_end()
}